Amid growing climate challenges and China’s “dual carbon” goals, promoting a green and low-carbon transition has become central to national energy policy. Carbon Emission Trading (CET) and Energy Consumption Right Trading (ECR), as market-based tools, have played positive roles in reducing emissions and improving energy efficiency, respectively. This paper analyzes the synergistic effects and dynamic evolution of CET and ECR policies on energy system transformation. Through an empirical analysis of Chinese provincial and municipal data from 2005 to 2022, this study finds that the CET policy is significant in promoting carbon reduction, while the ECR policy demonstrates a strong short-term constraint on improving energy efficiency. However, the synergistic effect of these two policies weakened over time, due to rising dual compliance costs and divergent policy objectives, this synergy gradually weakened and even led to friction. These findings underscore the need for coordinated and adaptive policy design to sustain synergy and support carbon goals.